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- What's new in Jalview 2.10 ?
+ What's new in Jalview 2.10.3 ?
- Jalview 2.10 is the next major release in the Jalview 2 series. Full
- details are in the Jalview
- 2.10 Release Notes, but the highlights are below.
+ Version 2.10.3 is due for release in October 2017. The full list of
+ bug fixes and new features can be found in the 2.10.3 Release Notes, but
+ the highlights are below.
+
+
+ Experimental Features
+
+
+ This release of Jalview introduces an Experimental Features
+ option in the Jalview Desktop's Tools menu that allows you
+ to try out features that are still in development. To access the
+ experimental features below - first enable the Tools→Enable
+ Experimental Features option, and then restart Jalview.
- - Ensembl sequence fetcher
Annotated
- Genes, transcripts and proteins can be retrieved via Jalview's new
- Ensembl REST
- client. Support for import of Ensembl data allows:
-
- - Aligned locus view
Transcripts
- retrieved for a gene identifier via the Ensembl or
- EnsemblGenomes sequence databases are automatically aligned to
- their reference genome, and introns hidden from the view.
- - Sequence variant data
Jalview
- propagates variant annotation on genomic regions onto
- transcripts and protein products, complete with associated
- metadata such as clinical significance.
-
- - Ensembl and ENA 'show cross-references'
- support
The Calculations menu's 'Show
- cross-references' now offers Ensembl as well as EMBLCDS and
- Uniprot when CDS/Protein mapping data is available for download or
- display. This allows variant annotation to be added directly to an
- alignment of UniProt sequences.
- - Working with structures
-
- - More accurate structure mappings
- Jalview now utilises the PDBe's SIFTS database (at EMBL-EBI)
- to match structures
- to UniProt sequences, even for structures containing
- multiple copies of a sequence.
- - Import structures as mmCIF
Jalview
- now downloads data from the EMBL-EBI's PDBe site as mmCIF. This allows very large
- structures to be imported, such as the HIV virus capsid
- assembly.
- - Chimera users will need to upgrade to
- 1.11.1
If you use Chimera to view structures
- downloaded by Jalview 2.10, you will need to make sure you are
- running the latest version of Chimera.
-
- - UniProt Free Text Search
The new
- search dialog for UniProt allows you to browse and retrieve
- sequences with free-text search, or structured queries.
- - Reference sequence alignment view
- Jalview 2.9 introduced support for reference sequences. In 2.10,
- when a reference sequence is defined for the alignment, the
- alignment column ruler is now numbered according to the reference
- sequence. The reference sequence for alignment views can also be
- saved and restored from Jalview projects.
+ - Annotation transfer between Chimera and Jalview
Two
+ new entries in
+ the Chimera viewer's Chimera menu allow positional annotation to
+ be exchanged between Chimera and Jalview.